Background: Pneumocystis jirovecii is responsible for Pneumocystis pneumonia (PCP), which occurs almost exclusively in immunocompromised individuals. Trimethoprim-sulfamethoxazole (TMP-SMZ) is regarded as the first-line treatment and prophylaxis for P. jirovecii infection, but the frequency of adverse reactions and newly emerged antibiotic resistance limit its use. Case presentation: Ulcerations and hemorrhages involving the tongue were noted secondary to TMP-SMZ desensitization against PCP in a 46-year-old male who had previously been diagnosed with IgA nephropathy and sustained prolonged corticosteroid therapy. There was an urgent need for an alternative regimen due to the severe response to TMP-SMZ. The patient was successfully treated with a combination therapy of caspofungin and clindamycin. Conclusion: Caspofungin combined with clindamycin is an optional treatment for PCP when treatment with TMP-SMZ fails or in patients who cannot tolerate TMP-SMZ.